I am a beginner in epigenetic analyses. I am using the Meffil package and pipeline in preprocessing my DNA methylation data. I performed QC, extracted SNPs, removed 4 outlier samples, ran clean QC and performed quantile normalization. For running the function below, this error occurs. The function does work for a subselection of the first 5 samples, when running a loop to find problematic samples, 4 samples come up, but cannot find why they are problematic and am not keep on removing them - besides; running the code previously went without errors (but now I ran QC with different cell type reference so have to repeat FN). Does anyone recognize this error, knows why it came to disturb, and even better - knows how to fix it? Thanks a million!

I am using an older version of R/RStudio because Meffil has not been updated yet.

> norm.objects <- meffil.normalize.quantiles(qc.objects, number.pcs=pc)

> norm.beta <- meffil.normalize.samples(norm.objects, cpglist.remove = qc.summary$bad.cpgs$name)
Error in rg.to.mu(rg, probes) : 
  all(c(probes.M.R$address, probes.U.R$address) %in% rownames(rg$R)) is not TRUE

> sessionInfo()
R version 4.3.3 (2024-02-29 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)

Matrix products: default


locale:
[1] LC_COLLATE=Dutch_Netherlands.utf8  LC_CTYPE=Dutch_Netherlands.utf8   
[3] LC_MONETARY=Dutch_Netherlands.utf8 LC_NUMERIC=C                      
[5] LC_TIME=Dutch_Netherlands.utf8    

time zone: Europe/Amsterdam
tzcode source: internal

attached base packages:
[1] parallel  stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] meffil_1.3.6          preprocessCore_1.62.1 SmartSVA_0.1.3        RSpectra_0.16-2      
 [5] isva_1.9              JADE_2.0-4            qvalue_2.32.0         gdsfmt_1.36.1        
 [9] statmod_1.5.0         quadprog_1.5-8        DNAcopy_1.74.1        fastICA_1.2-7        
[13] lme4_1.1-36           Matrix_1.6-3          multcomp_1.4-26       TH.data_1.1-3        
[17] survival_3.5-8        mvtnorm_1.3-3         matrixStats_1.5.0     markdown_1.13        
[21] gridExtra_2.3         Cairo_1.6-2           knitr_1.49            reshape2_1.4.4       
[25] plyr_1.8.9            sva_3.48.0            BiocParallel_1.34.2   genefilter_1.82.1    
[29] mgcv_1.9-1            nlme_3.1-164          limma_3.56.2          sandwich_3.1-1       
[33] lmtest_0.9-40         zoo_1.8-12            MASS_7.3-60.0.1       illuminaio_0.42.0    
[37] tidyr_1.3.1           dplyr_1.1.4           ggplot2_3.5.1         devtools_2.4.5       
[41] usethis_3.1.0         BiocManager_1.30.25  

loaded via a namespace (and not attached):
 [1] Rdpack_2.6.2            DBI_1.2.3               bitops_1.0-9           
 [4] remotes_2.5.0           rlang_1.1.2             magrittr_2.0.3         
 [7] clue_0.3-66             compiler_4.3.3          RSQLite_2.3.9          
[10] png_0.1-8               vctrs_0.6.4             stringr_1.5.1          
[13] profvis_0.4.0           pkgconfig_2.0.3         crayon_1.5.3           
[16] fastmap_1.2.0           XVector_0.40.0          ellipsis_0.3.2         
[19] promises_1.3.2          sessioninfo_1.2.2       nloptr_2.1.1           
[22] purrr_1.0.2             bit_4.5.0.1             xfun_0.50              
[25] zlibbioc_1.46.0         cachem_1.1.0            GenomeInfoDb_1.36.4    
[28] blob_1.2.4              later_1.4.1             cluster_2.1.6          
[31] R6_2.5.1                stringi_1.8.4           boot_1.3-29            
[34] pkgload_1.4.0           Rcpp_1.0.14             IRanges_2.34.1         
[37] httpuv_1.6.15           splines_4.3.3           tidyselect_1.2.1       
[40] rstudioapi_0.17.1       codetools_0.2-19        miniUI_0.1.1.1         
[43] pkgbuild_1.4.6          lattice_0.22-5          tibble_3.2.1           
[46] Biobase_2.60.0          shiny_1.10.0            withr_3.0.2            
[49] KEGGREST_1.40.1         askpass_1.2.1           evaluate_1.0.3         
[52] urlchecker_1.0.1        Biostrings_2.68.1       pillar_1.10.1          
[55] MatrixGenerics_1.14.0   stats4_4.3.3            reformulas_0.4.0       
[58] generics_0.1.3          RCurl_1.98-1.16         S4Vectors_0.38.2       
[61] munsell_0.5.1           scales_1.3.0            minqa_1.2.8            
[64] xtable_1.8-4            glue_1.6.2              tools_4.3.3            
[67] annotate_1.78.0         locfit_1.5-9.10         fs_1.6.5               
[70] XML_3.99-0.18           grid_4.3.3              rbibutils_2.3          
[73] AnnotationDbi_1.62.2    edgeR_3.42.4            colorspace_2.1-1       
[76] base64_2.0.2            GenomeInfoDbData_1.2.10 cli_3.6.1              
[79] gtable_0.3.6            digest_0.6.37           BiocGenerics_0.46.0    
[82] htmlwidgets_1.6.4       memoise_2.0.1           htmltools_0.5.8.1      
[85] lifecycle_1.0.4         httr_1.4.7              mime_0.12              
[88] openssl_2.3.1           bit64_4.6.0-1